}
/***********************************************************************/
int ReadTree::readSpecialChar(istream& f, char c, string name) {
}
/***********************************************************************/
int ReadTree::readSpecialChar(istream& f, char c, string name) {
}
/**************************************************************************************************/
//This function read the file through the translation of the sequences names and updates treemap.
}
/**************************************************************************************************/
//This function read the file through the translation of the sequences names and updates treemap.
n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off
lc = readNewickInt(filehandle, n, T);
n = numLeaves; //number of leaves / sequences, we want node 1 to start where the leaves left off
lc = readNewickInt(filehandle, n, T);
if(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
if(filehandle.peek()==','){
readSpecialChar(filehandle,',',"comma");
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
if(filehandle.peek() == ')'){
readSpecialChar(filehandle,')',"right parenthesis");
}
if(rooted != 1){
T->tree[n].setChildren(lc,rc);
T->tree[n].setBranchLength(0);
if(rooted != 1){
T->tree[n].setChildren(lc,rc);
T->tree[n].setBranchLength(0);
}
/**************************************************************************************************/
int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
try {
}
/**************************************************************************************************/
int ReadNewickTree::readNewickInt(istream& f, int& n, Tree* T) {
try {
if (rc == -1) { return -1; } //reports an error in reading
if(f.peek()==')'){
readSpecialChar(f,')',"right parenthesis");
if (rc == -1) { return -1; } //reports an error in reading
if(f.peek()==')'){
readSpecialChar(f,')',"right parenthesis");
T->tree[n].setChildren(lc,rc);
T->tree[lc].setParent(n);
T->tree[n].setChildren(lc,rc);
T->tree[lc].setParent(n);
globaldata->gTreemap->namesOfSeqs.push_back(name);
globaldata->gTreemap->treemap[name].groupname = "xxx";
globaldata->gTreemap->namesOfSeqs.push_back(name);
globaldata->gTreemap->treemap[name].groupname = "xxx";
}
/**************************************************************************************************/
/**************************************************************************************************/
}
/**************************************************************************************************/
/**************************************************************************************************/